1
|
Arnold PR, Wen M, Zhang L, Ying Y, Xiao X, Chu X, Wang G, Zhang X, Mao Z, Zhang A, Hamilton DJ, Chen W, Li XC. Suppression of FOXP3 expression by the AP-1 family transcription factor BATF3 requires partnering with IRF4. Front Immunol 2022; 13:966364. [PMID: 36090981 PMCID: PMC9452699 DOI: 10.3389/fimmu.2022.966364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
FOXP3 is the lineage-defining transcription factor for Tregs, a cell type critical to immune tolerance, but the mechanisms that control FOXP3 expression in Tregs remain incompletely defined, particularly as it relates to signals downstream of TCR and CD28 signaling. Herein, we studied the role of IRF4 and BATF3, two transcription factors upregulated upon T cell activation, to the conversion of conventional CD4+ T cells to FOXP3+ T cells (iTregs) in vitro. We found that IRF4 must partner with BATF3 to bind to a regulatory region in the Foxp3 locus where they cooperatively repress FOXP3 expression and iTreg induction. In addition, we found that interactions of these transcription factors are necessary for glycolytic reprogramming of activated T cells that is antagonistic to FOXP3 expression and stability. As a result, Irf4 KO iTregs show increased demethylation of the critical CNS2 region in the Foxp3 locus. Together, our findings provide important insights how BATF3 and IRF4 interactions integrate activating signals to control CD4+ cell fate decisions and govern Foxp3 expression.
Collapse
Affiliation(s)
- Preston R. Arnold
- College of Medicine, Texas A&M Health, Bryan, TX, United States
- Immunobiology and Transplant Science Center and Department of Surgery, Houston Methodist Hospital, Texas Medical Center, Houston, TX, United States
| | - Mou Wen
- Immunobiology and Transplant Science Center and Department of Surgery, Houston Methodist Hospital, Texas Medical Center, Houston, TX, United States
| | - Lei Zhang
- Immunobiology and Transplant Science Center and Department of Surgery, Houston Methodist Hospital, Texas Medical Center, Houston, TX, United States
| | - Yuanlin Ying
- Immunobiology and Transplant Science Center and Department of Surgery, Houston Methodist Hospital, Texas Medical Center, Houston, TX, United States
| | - Xiang Xiao
- Immunobiology and Transplant Science Center and Department of Surgery, Houston Methodist Hospital, Texas Medical Center, Houston, TX, United States
| | - Xiufeng Chu
- Immunobiology and Transplant Science Center and Department of Surgery, Houston Methodist Hospital, Texas Medical Center, Houston, TX, United States
| | - Guangchuan Wang
- Immunobiology and Transplant Science Center and Department of Surgery, Houston Methodist Hospital, Texas Medical Center, Houston, TX, United States
| | - Xiaolong Zhang
- Immunobiology and Transplant Science Center and Department of Surgery, Houston Methodist Hospital, Texas Medical Center, Houston, TX, United States
| | - Zhuyun Mao
- Immunobiology and Transplant Science Center and Department of Surgery, Houston Methodist Hospital, Texas Medical Center, Houston, TX, United States
| | - Aijun Zhang
- Department of Medicine, Houston Methodist, Weill Cornell Medicine Affiliate, Houston, TX, United States
- Center for Bioenergetics, Houston Methodist Hospital and Research Institute, Texas Medical Center, Houston, TX, United States
- Weill Cornell Medical College of Cornell University, New York, NY, United States
| | - Dale J. Hamilton
- Department of Medicine, Houston Methodist, Weill Cornell Medicine Affiliate, Houston, TX, United States
- Center for Bioenergetics, Houston Methodist Hospital and Research Institute, Texas Medical Center, Houston, TX, United States
- Weill Cornell Medical College of Cornell University, New York, NY, United States
| | - Wenhao Chen
- Immunobiology and Transplant Science Center and Department of Surgery, Houston Methodist Hospital, Texas Medical Center, Houston, TX, United States
- Department of Surgery, Weill Cornell Medical College of Cornell University, New York, NY, United States
| | - Xian C. Li
- Immunobiology and Transplant Science Center and Department of Surgery, Houston Methodist Hospital, Texas Medical Center, Houston, TX, United States
- Department of Surgery, Weill Cornell Medical College of Cornell University, New York, NY, United States
- *Correspondence: Xian C. Li,
| |
Collapse
|
2
|
de Klerk DJ, de Keijzer MJ, Dias LM, Heemskerk J, de Haan LR, Kleijn TG, Franchi LP, Heger M. Strategies for Improving Photodynamic Therapy Through Pharmacological Modulation of the Immediate Early Stress Response. Methods Mol Biol 2022; 2451:405-480. [PMID: 35505025 DOI: 10.1007/978-1-0716-2099-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Photodynamic therapy (PDT) is a minimally to noninvasive treatment modality that has emerged as a promising alternative to conventional cancer treatments. PDT induces hyperoxidative stress and disrupts cellular homeostasis in photosensitized cancer cells, resulting in cell death and ultimately removal of the tumor. However, various survival pathways can be activated in sublethally afflicted cancer cells following PDT. The acute stress response is one of the known survival pathways in PDT, which is activated by reactive oxygen species and signals via ASK-1 (directly) or via TNFR (indirectly). The acute stress response can activate various other survival pathways that may entail antioxidant, pro-inflammatory, angiogenic, and proteotoxic stress responses that culminate in the cancer cell's ability to cope with redox stress and oxidative damage. This review provides an overview of the immediate early stress response in the context of PDT, mechanisms of activation by PDT, and molecular intervention strategies aimed at inhibiting survival signaling and improving PDT outcome.
Collapse
Affiliation(s)
- Daniel J de Klerk
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Mark J de Keijzer
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Lionel M Dias
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Faculdade de Ciências da Saúde (FCS-UBI), Universidade da Beira Interior, Covilhã, Portugal
| | - Jordi Heemskerk
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
| | - Lianne R de Haan
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Tony G Kleijn
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Leonardo P Franchi
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas (ICB) 2, Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil
- Faculty of Philosophy, Department of Chemistry, Center of Nanotechnology and Tissue Engineering-Photobiology and Photomedicine Research Group, Sciences, and Letters of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Michal Heger
- Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, Department of Pharmaceutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, People's Republic of China.
- Laboratory of Experimental Oncology, Department of Pathology, Erasmus MC, Rotterdam, The Netherlands.
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.
| |
Collapse
|
3
|
IFP35 Is a Relevant Factor in Innate Immunity, Multiple Sclerosis, and Other Chronic Inflammatory Diseases: A Review. BIOLOGY 2021; 10:biology10121325. [PMID: 34943240 PMCID: PMC8698480 DOI: 10.3390/biology10121325] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 02/03/2023]
Abstract
Simple Summary In this review, we focused on the emerging role of IFP35, a highly conserved leucine zipper protein from fish to humans, with a still unknown biological function. The considered literature indicates this protein as a key-pleiotropic factor reflecting JAK-STAT and DAMPs pathways activation in innate immunity-dependent inflammation, as well as in the physiology and general pathology of a wide range of phylogenetically distant organisms. These findings also indicate IFP35 as a biologically relevant molecule in human demyelinating diseases of the central nervous system, including Multiple Sclerosis, and other organ-specific chronic inflammatory disorders. Abstract Discovered in 1993 by Bange et al., the 35-kDa interferon-induced protein (IFP35) is a highly conserved cytosolic interferon-induced leucine zipper protein with a 17q12-21 coding gene and unknown function. Belonging to interferon stimulated genes (ISG), the IFP35 reflects the type I interferon (IFN) activity induced through the JAK-STAT phosphorylation, and it can homodimerize with N-myc-interactor (NMI) and basic leucine zipper transcription factor (BATF), resulting in nuclear translocation and a functional expression. Casein kinase 2-interacting protein-1 (CKIP-1), retinoic acid-inducible gene I (RIG-I), and laboratory of genetics and physiology 2 Epinephelus coioides (EcLGP2) are thought to regulate IFP35, via the innate immunity pathway. Several in vitro and in vivo studies on fish and mammals have confirmed the IFP35 as an ISG factor with antiviral and antiproliferative functions. However, in a mice model of sepsis, IFP35 was found working as a damage associated molecular pattern (DAMP) molecule, which enhances inflammation by acting in the innate immune-mediated way. In human pathology, the IFP35 expression level predicts disease outcome and response to therapy in Multiple Sclerosis (MS), reflecting IFN activity. Specifically, IFP35 was upregulated in Lupus Nephritis (LN), Rheumatoid Arthritis (RA), and untreated MS. However, it normalized in the MS patients undergoing therapy. The considered data indicate IFP35 as a pleiotropic factor, suggesting it as biologically relevant in the innate immunity, general pathology, and human demyelinating diseases of the central nervous system.
Collapse
|
4
|
Katagiri T, Kameda H, Nakano H, Yamazaki S. Regulation of T cell differentiation by the AP-1 transcription factor JunB. Immunol Med 2021; 44:197-203. [PMID: 33470914 DOI: 10.1080/25785826.2021.1872838] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
JunB, a component of the activator protein-1 (AP-1) transcription factor, is known to exhibit an important role in bone formation and bone marrow cell proliferation. During T helper type 2 (Th2) cell differentiation, JunB contributes to the regulation of interleukin (IL)-4 expression, and AP-1 and nuclear factor of activated T cell (NFAT) constitute a heteromer and contribute to IL-2 production. However, the role of JunB in other T cells has not been investigated. In 2017, it was revealed that JunB, in collaboration with basic leucine zipper ATF-like transcription factor (BATF), regulates the expression of Th17-related genes. Furthermore, JunB was found to play an important role in regulatory T (Treg) cell differentiation, contributing to CD25 expression and IL-2 production. IL-2 is a T cell activator and has been shown as a necessary factor for Treg proliferation. Here, we review the role of JunB in T cells based on basic research data and discuss the potential for its clinical applications.
Collapse
Affiliation(s)
- Takaharu Katagiri
- Department of Biochemistry, Toho University School of Medicine, Tokyo, Japan.,Faculty of Medicine, Division of Rheumatology, Department of Internal Medicine, Ohashi Medical Center, Toho University, Tokyo, Japan
| | - Hideto Kameda
- Faculty of Medicine, Division of Rheumatology, Department of Internal Medicine, Ohashi Medical Center, Toho University, Tokyo, Japan
| | - Hiroyasu Nakano
- Department of Biochemistry, Toho University School of Medicine, Tokyo, Japan
| | - Soh Yamazaki
- Department of Biochemistry, Toho University School of Medicine, Tokyo, Japan
| |
Collapse
|
5
|
Bartko JC, Li Y, Sun G, Halterman MW. Phosphorylation within the bipartite NLS alters the localization and toxicity of the ER stress response factor DDIT3/CHOP. Cell Signal 2020; 74:109713. [PMID: 32673756 DOI: 10.1016/j.cellsig.2020.109713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/06/2020] [Accepted: 07/09/2020] [Indexed: 02/04/2023]
Abstract
Regulated nuclear-cytoplasmic trafficking is a well-established mechanism utilized by cells to regulate adaptive and maladaptive responses to acute oxidant stress. Commonly associated with endoplasmic reticulum stress, the bZIP transcription factor CCAAT/enhancer-binding protein homologous protein (CHOP/DDIT3) mediates the cellular response to redox stress with effects on cellular growth, differentiation, and survival. We show through functional analyses that CHOP contains a conserved, compound pat4/bipartite nuclear localization signal within the basic DNA-binding domain. Using phylogenetic analyses and mass spectrometry, we now show that Ser107 located within the linker region of the bipartite NLS domain is a substrate for phosphorylation under standard culture conditions. Studies using the S107E phospho-mimic of CHOP indicate that changes in the charge properties at this residue regulate CHOP's nuclear-to-cytoplasmic ratio. And while co-stimulation with the SERCA inhibitor thapsigargin induced injury in cells expressing wild-type CHOP, the S107A point-mutant blocked this response. These findings indicate that phosphorylation within the bipartite NLS exerts regulatory effects on both the subcellular localization and toxic potential of DDIT3/CHOP. Future studies geared towards defining the relevant kinase/phosphatase networks that converge on the phosphorylation-regulated NLS (prNLS) phosphoepitope may provide an opportunity to constrain cellular damage in the context of acute ER stress.
Collapse
Affiliation(s)
- Jonathan C Bartko
- Departments of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - Yinghui Li
- Department of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - George Sun
- Department of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - Marc W Halterman
- Department of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States; Department of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States.
| |
Collapse
|
6
|
Joo J, Lee YH, Song SI. OsbZIP42 is a positive regulator of ABA signaling and confers drought tolerance to rice. PLANTA 2019; 249:1521-1533. [PMID: 30712129 DOI: 10.1007/s00425-019-03104-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/30/2019] [Indexed: 05/21/2023]
Abstract
OsbZIP42 is a positive regulator of ABA signaling and drought stress tolerance. The activation of OsbZIP42 depends on stress-/ABA-activated protein kinase 4 (SAPK4) and an additional ABA-dependent modification of OsbZIP42. Basic leucine zipper transcription factors (bZIP TFs) play important roles in the ABA signaling pathway in plants. Rice OsbZIP42 is a member of the group E bZIP, which is an ortholog of Arabidopsis group A bZIP. This latter group includes abscisic acid-responsive element (ABRE)-binding factors (ABFs) involved in abiotic stress tolerance. The expression of OsbZIP42 was induced by ABA treatment, although it was not induced by drought and salt stresses. Unlike other bZIP TFs, OsbZIP42 contained two transcriptional activation domains. Although the full-length OsbZIP42 protein did not, the N-terminus of the protein interacted with SAPK4. Our results suggest that the activation of OsbZIP42 by SAPK4 requires another ABA-dependent modification of OsbZIP42. Transgenic rice overexpressing OsbZIP42 (OsbZIP42-OX) exhibited a rapidly elevated expression of the ABA-responsive LEA3 and Rab16 genes and was hypersensitive to ABA. Analyses of the OsbZIP42-OX plants revealed enhanced tolerance to drought stress. These results suggest that OsbZIP42 is a positive regulator of ABA signaling and drought stress tolerance depending on its activation, which is followed by an additional ABA-dependent modification. We propose that OsbZIP42 is an important player in rice for conferring ABA-dependent drought tolerance.
Collapse
Affiliation(s)
- Joungsu Joo
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, 449-728, Korea
| | - Youn Hab Lee
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, 449-728, Korea
| | - Sang Ik Song
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, 449-728, Korea.
| |
Collapse
|
7
|
Wang LM, Zhang B, Li JJ, Zhou YC, Wang DX. The expression change of RORγt, BATF, and IL-17 in Chinese vitiligo patients with 308 nanometers excimer laser treatment. Dermatol Ther 2018; 31:e12598. [PMID: 29642271 DOI: 10.1111/dth.12598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/21/2017] [Accepted: 03/18/2018] [Indexed: 11/29/2022]
Abstract
This study aims to explore the expression of RORγt, BATF, and IL-17 in Chinese vitiligo patients with 308 nm excimer laser treatment. One hundred and sixty-four vitiligo patients treated with 308 nm excimer laser were enrolled as Case group and 137 health examiners as Control group. Quantitative real-time polymerase chain reaction and immunohistochemistry were conducted to detect the expressions of RORγt, BATF, and IL-17. Expression of RORγt, BATF, IL-17A, and IL-17F were higher in Case group than Control group, with the diagnostic accuracy of 88.04, 87.38, 97.34, and 89.04%, respectively. Pearson correlation analysis showed a positive correlation in RORγt, BATF, IL-17A, and IL-17F mRNAs in vitiligo patients. Moreover, their expressions were higher in active vitiligo patients than stable ones. Besides, the expressions of RORγt, BATF, IL-17A, and IL-17F in vitiligo skin were significantly higher than those in non lesional skin and normal controls. After treatment, their expressions were significantly decreased. Active vitiligo and the high expressions of RORγt, BATF, and IL-17F were the independent risk factors for the ineffectiveness of 308 nm excimer laser treatment. The expressions of RORγt, BATF, IL-17 were significantly enhanced in vitiligo patients, which were correlated with the activity of vitiligo and 308 nm excimer laser therapeutic effects.
Collapse
Affiliation(s)
- Lu-Mei Wang
- Department of Dermatology, Dong Guan People's Hospital, Guangdong Province, Dongguan 523018, People's Republic of China
| | - Bin Zhang
- Department of Gynaecology and Obstetrics, Dong Guan People's Hospital, Guangdong Province, Dongguan 523018, People's Republic of China
| | - Jun-Jie Li
- Department of Dermatology, Dong Guan People's Hospital, Guangdong Province, Dongguan 523018, People's Republic of China
| | - Yun-Cong Zhou
- Department of Dermatology, Dong Guan People's Hospital, Guangdong Province, Dongguan 523018, People's Republic of China
| | - Dong-Xia Wang
- Department of Interventional Therapy, Dong Guan People's Hospital, Guangdong Province, Dongguan 523018, People's Republic of China
| |
Collapse
|
8
|
Kuwahara M, Ise W, Ochi M, Suzuki J, Kometani K, Maruyama S, Izumoto M, Matsumoto A, Takemori N, Takemori A, Shinoda K, Nakayama T, Ohara O, Yasukawa M, Sawasaki T, Kurosaki T, Yamashita M. Bach2-Batf interactions control Th2-type immune response by regulating the IL-4 amplification loop. Nat Commun 2016; 7:12596. [PMID: 27581382 PMCID: PMC5025763 DOI: 10.1038/ncomms12596] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/08/2016] [Indexed: 12/17/2022] Open
Abstract
Although Bach2 has an important role in regulating the Th2-type immune response, the underlying molecular mechanisms remain unclear. We herein demonstrate that Bach2 associates with Batf and binds to the regulatory regions of the Th2 cytokine gene loci. The Bach2–Batf complex antagonizes the recruitment of the Batf–Irf4 complex to AP-1 motifs and suppresses Th2 cytokine production. Furthermore, we find that Bach2 regulates the Batf and Batf3 expressions via two distinct pathways. First, Bach2 suppresses the maintenance of the Batf and Batf3 expression through the inhibition of IL-4 production. Second, the Bach2–Batf complex directly binds to the Batf and Batf3 gene loci and reduces transcription by interfering with the Batf–Irf4 complex. These findings suggest that IL-4 and Batf form a positive feedback amplification loop to induce Th2 cell differentiation and the subsequent Th2-type immune response, and Bach2–Batf interactions are required to prevent an excessive Th2 response. Bach2 limits T cell effector functions. Here the authors show that Bach2–Batf complex antagonizes the recruitment of the Batf–Irf4 complex to AP-1 motifs and suppresses Th2 cytokine production, and describe mechanisms of negative feedback by which Bach2 restricts Baft-mediated Th2 response.
Collapse
Affiliation(s)
- Makoto Kuwahara
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan.,Department of Translational Immunology, Translational Research Center, Ehime University Hospital, Shitsukawa, Toon, Ehime 791-0295, Japan.,Division of Immune Regulation, Department of Proteo-Inovation, Proteo-Science Center, Ehime University, Toon, Ehime 791-0295, Japan
| | - Wataru Ise
- Department of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Mizuki Ochi
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan.,Division of Cell-Free Sciences, Department of Proteo-Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Junpei Suzuki
- Department of Translational Immunology, Translational Research Center, Ehime University Hospital, Shitsukawa, Toon, Ehime 791-0295, Japan.,Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Kohei Kometani
- Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, 1-7-22 suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Saho Maruyama
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Maya Izumoto
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Akira Matsumoto
- Department of Infection and Host Defenses, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Nobuaki Takemori
- Division of Proteomics, Department of Proteo-Medicine, Proteo-Science Center, Ehime University, Toon, Ehime 791-0295, Japan
| | - Ayako Takemori
- Division of Proteomics, Department of Proteo-Medicine, Proteo-Science Center, Ehime University, Toon, Ehime 791-0295, Japan
| | - Kenta Shinoda
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670 Japan
| | - Osamu Ohara
- Human DNA Analysis Group, Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Masaki Yasukawa
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Sciences, Department of Proteo-Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Tomohiro Kurosaki
- Department of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.,Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, 1-7-22 suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Masakatsu Yamashita
- Department of Immunology, Graduate School of Medicine, Ehime University, Shitsukawa, Toon, Ehime 791-0295, Japan.,Department of Translational Immunology, Translational Research Center, Ehime University Hospital, Shitsukawa, Toon, Ehime 791-0295, Japan.,Division of Immune Regulation, Department of Proteo-Inovation, Proteo-Science Center, Ehime University, Toon, Ehime 791-0295, Japan
| |
Collapse
|
9
|
Sopel N, Graser A, Mousset S, Finotto S. The transcription factor BATF modulates cytokine-mediated responses in T cells. Cytokine Growth Factor Rev 2016; 30:39-45. [PMID: 26970726 DOI: 10.1016/j.cytogfr.2016.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The transcription factor BATF (basic leucine zipper transcription factor, ATF-like), belongs to the AP-1 family of transcription factors and has been shown to be predominantly expressed in cells of haematopoietic origin, especially in B and T cells. In studies using Batf-deficient mice, a profound defect in the differentiation of T helper cells type 17 (Th17) and follicular T helper cells (Tfh) was described, as well as an impairment of antibody production with switched isotypes. More recently BATF has been described to influence also Th2 and Th9 responses in models of murine experimental asthma. In CD8(+) T cells BATF has been found associated with anti-viral responses. This review summarizes the role of BATF in CD4(+) T cell subsets and in CD8(+) T cells, with particular focus on this transcription factor in the setting of allergic asthma.
Collapse
Affiliation(s)
- Nina Sopel
- Department of Molecular Pneumology, Friedrich-Alexander University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Anna Graser
- Department of Molecular Pneumology, Friedrich-Alexander University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Stephanie Mousset
- Department of Molecular Pneumology, Friedrich-Alexander University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Susetta Finotto
- Department of Molecular Pneumology, Friedrich-Alexander University Erlangen-Nürnberg, 91052 Erlangen, Germany.
| |
Collapse
|
10
|
Llorca CM, Potschin M, Zentgraf U. bZIPs and WRKYs: two large transcription factor families executing two different functional strategies. FRONTIERS IN PLANT SCIENCE 2014; 5:169. [PMID: 24817872 PMCID: PMC4012195 DOI: 10.3389/fpls.2014.00169] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/08/2014] [Indexed: 05/20/2023]
Abstract
bZIPs and WRKYs are two important plant transcription factor (TF) families regulating diverse developmental and stress-related processes. Since a partial overlap in these biological processes is obvious, it can be speculated that they fulfill non-redundant functions in a complex regulatory network. Here, we focus on the regulatory mechanisms that are so far described for bZIPs and WRKYs. bZIP factors need to heterodimerize for DNA-binding and regulation of transcription, and based on a bioinformatics approach, bZIPs can build up more than the double of protein interactions than WRKYs. In contrast, an enrichment of the WRKY DNA-binding motifs can be found in WRKY promoters, a phenomenon which is not observed for the bZIP family. Thus, the two TF families follow two different functional strategies in which WRKYs regulate each other's transcription in a transcriptional network whereas bZIP action relies on intensive heterodimerization.
Collapse
Affiliation(s)
| | | | - Ulrike Zentgraf
- *Correspondence: Ulrike Zentgraf, Department of General Genetics, Center of Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany e-mail:
| |
Collapse
|
11
|
Specificity through cooperation: BATF-IRF interactions control immune-regulatory networks. Nat Rev Immunol 2013; 13:499-509. [PMID: 23787991 DOI: 10.1038/nri3470] [Citation(s) in RCA: 269] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Basic leucine zipper transcription factor ATF-like (BATF), BATF2 and BATF3 belong to the activator protein 1 (AP-1) family of transcription factors, which regulate numerous cellular processes. Initially, BATF family members were thought to function only as inhibitors of AP-1-driven transcription, but recent studies have uncovered that these factors have unique, non-redundant and positive transcriptional activities in dendritic cells, B cells and T cells. The question of how BATF and BATF3 - which lack a transcriptional activation domain, unlike the AP-1 factors FOS and JUN - can exert unique positive transcriptional specificity has now been answered by the discovery that BATF molecules interact with members of the interferon-regulatory factor (IRF) family. The capacity of the BATF leucine zipper regions to mediate dimerization with AP-1 factors and also to define cooperative interactions with heterologous factors explains both the positive transcriptional activity of BATF proteins and how they activate distinct sets of target genes compared with FOS.
Collapse
|
12
|
Cortese MS, Etxebeste O, Garzia A, Espeso EA, Ugalde U. Elucidation of functional markers from Aspergillus nidulans developmental regulator FlbB and their phylogenetic distribution. PLoS One 2011; 6:e17505. [PMID: 21423749 PMCID: PMC3053368 DOI: 10.1371/journal.pone.0017505] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 02/06/2011] [Indexed: 11/18/2022] Open
Abstract
Aspergillus nidulans is a filamentous fungus widely used as a model for biotechnological and clinical research. It is also used as a platform for the study of basic eukaryotic developmental processes. Previous studies identified and partially characterized a set of proteins controlling cellular transformations in this ascomycete. Among these proteins, the bZip type transcription factor FlbB is a key regulator of reproduction, stress responses and cell-death. Our aim here was the prediction, through various bioinformatic methods, of key functional residues and motifs within FlbB in order to inform the design of future laboratory experiments and further the understanding of the molecular mechanisms that control fungal development. A dataset of FlbB orthologs and those of its key interaction partner FlbE was assembled from 40 members of the Pezizomycotina. Unique features were identified in each of the three structural domains of FlbB. The N-terminal region encoded a bZip transcription factor domain with a novel histidine-containing DNA binding motif while the dimerization determinants exhibited two distinct profiles that segregated by class. The C-terminal region of FlbB showed high similarity with the AP-1 family of stress response regulators but with variable patterns of conserved cysteines that segregated by class and order. Motif conservation analysis revealed that nine FlbB orthologs belonging to the Eurotiales order contained a motif in the central region that could mediate interaction with FlbE. The key residues and motifs identified here provide a basis for the design of follow-up experimental investigations. Additionally, the presence or absence of these residues and motifs among the FlbB orthologs could help explain the differences in the developmental programs among fungal species as well as define putative complementation groups that could serve to extend known functional characterizations to other species.
Collapse
Affiliation(s)
- Marc S Cortese
- Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country, San Sebastián, Spain.
| | | | | | | | | |
Collapse
|
13
|
Liao J, Humphrey SE, Poston S, Taparowsky EJ. Batf promotes growth arrest and terminal differentiation of mouse myeloid leukemia cells. Mol Cancer Res 2011; 9:350-63. [PMID: 21296860 DOI: 10.1158/1541-7786.mcr-10-0375] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Batf is a basic leucine zipper transcription factor belonging to the activator protein-1 superfamily. Batf expression is regulated following stimulation of both lymphoid and myeloid cells. When treated with leukemia inhibitory factor, mouse M1 myeloid leukemia cells commit to a macrophage differentiation program that is dependent on Stat3 and involves the induction of Batf gene transcription via the binding of Stat3 to the Batf promoter. RNA interference was employed to block Batf induction in this system and the cells failed to growth arrest or to terminally differentiate. Restoring Batf expression not only reversed the differentiation-defective phenotype but also caused the cells to display signs of spontaneous differentiation in the absence of stimulation. Efforts to define genetic targets of the Batf transcription factor in M1 cells led to the identification of c-myb, a proto-oncogene known to promote blood cell proliferation and to inhibit the differentiation of M1 cells. These results provide strong evidence that Batf mediates the differentiation-inducing effects of Stat3 signaling in M1 cells and suggest that Batf may play a similar role in other blood cell lineages where alterations to the Jak-Stat pathway are hallmarks of disrupted development and disease.
Collapse
Affiliation(s)
- Juan Liao
- Department of Biological Sciences, 201 South University Street, West Lafayette, IN 47907-2064, USA
| | | | | | | |
Collapse
|
14
|
Hong JY, Chae MJ, Lee IS, Lee YN, Nam MH, Kim DY, Byun MO, Yoon IS. Phosphorylation-mediated regulation of a rice ABA responsive element binding factor. PHYTOCHEMISTRY 2011; 72:27-36. [PMID: 21055780 DOI: 10.1016/j.phytochem.2010.10.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 07/26/2010] [Accepted: 10/04/2010] [Indexed: 05/17/2023]
Abstract
OREB1 is a rice ABRE binding factor characterized by the presence of multiple highly-conserved phosphorylation domains (C1, C2, C3, and C4) and two kinase recognition motifs, RXXS/T and S/TXXE/D, within different functional domains. An in vitro kinase assay showed that OREB1 is phosphorylated not only by the SnRK2 kinase, but also by other Ser/Thr protein kinases, such as CaMKII, CKII, and SnRK3. Furthermore, the N-terminal phosphorylation domain C1 was found to be differentially phosphorylated by the SnRK2/SnRK3 kinase and by hyperosmotic/cold stress, suggesting that the C1 domain may function in decoding different signals. The phosphorylation-mediated regulation of OREB1 activity was investigated through mutation of the SnRK2 recognition motif RXXS/T within each phosphorylation module. OREB1 contains a crucial nine-amino acid transactivation domain located near the phosphorylation module C1. Deletion of the C1 domain increased OREB1 activity, whereas mutation of Ser 44, Ser 45, and Ser 48 of the C1 domain to aspartates decreased OREB1 activity. In the C2 domain, a double mutation of Ser 118 and Ser 120 to alanines suppressed OREB1 activity. These findings strongly suggest that selective phosphorylation of the C1 or C2 modules may positively or negatively regulate OREB1 transactivation. In addition, mutation of Ser 385 of the C4 domain to alanines completely abolished the interaction between OREB1 and a rice 14-3-3 protein, GF14d, suggesting that SnRK2-mediated phosphorylation may regulate this interaction. These results indicate that phosphorylation domains of OREB1 are not functionally redundant and regulate at least three different functions, including transactivation activity, DNA binding, and protein interactions. The multisite phosphorylation of OREB1 is likely a key for the fine control of its activity and signal integration in the complex stress signaling network of plant cells.
Collapse
Affiliation(s)
- Ji Yeon Hong
- Bio-Crops Development Division, National Academy of Agricultural Sciences, Suwon, Republic of Korea
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Abstract
The third lineage of T helper subsets, Th17, has recently been identified as an IL- 17-producing CD4+ Th cell, and its functions and regulatory mechanisms have been extensively characterized in immune responses. Functional studies have provided evidence that Th17 cells are important for the modulation of autoimmune responses, such as chronic asthma, rheumatoid arthritis, inflammatory bowel diseases, and multiple sclerosis. Murine Th17 cell differentiation is enhanced by the coordinated functions of distinct cytokines including TGFbeta, IL-6, IL-21, and IL-23, whereas IL-2, IL-4, IFNgamma, and IL-27 inhibit its differentiation. In addition, Th17 cells are controlled by several transcription factors such as RORgammat, IRF4, BATF, FoxP3, T-bet, PPARgamma, E-FABP, and SOCSs. This review focuses on the functions and regulatory mechanisms of several transcription factors in the control of Th17 cell differentiation.
Collapse
Affiliation(s)
- Eun Sook Hwang
- Division of Life and Pharmaceutical Sciences, College of Phamacy, Ewha Womans University, Center for Cell Signaling and Drug Discovery Research, 11-1 Daehyeon-dong, Seodaemun-gu, Seoul 120-750, Korea.
| |
Collapse
|
16
|
Abstract
The past two decades revealed a plethora of Ca2+-responsive proteins and downstream targets in plants, of which several are unique to plants. More recent high-throughput 'omics' approaches and bioinformatics are exposing Ca2+-responsive cis-elements and the corresponding Ca2+-responsive genes. Here, we review the current knowledge on Ca2+-signaling pathways that regulate gene expression in plants, and we link these to mechanisms by which plants respond to biotic and abiotic stresses.
Collapse
Affiliation(s)
- Yael Galon
- Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel-Aviv University 69978, Tel-Aviv, Israel
| | | | | |
Collapse
|
17
|
Kirchler T, Briesemeister S, Singer M, Schütze K, Keinath M, Kohlbacher O, Vicente-Carbajosa J, Teige M, Harter K, Chaban C. The role of phosphorylatable serine residues in the DNA-binding domain of Arabidopsis bZIP transcription factors. Eur J Cell Biol 2010; 89:175-83. [DOI: 10.1016/j.ejcb.2009.11.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
18
|
Li G, Li W, Angelastro JM, Greene LA, Liu DX. Identification of a novel DNA binding site and a transcriptional target for activating transcription factor 5 in c6 glioma and mcf-7 breast cancer cells. Mol Cancer Res 2009; 7:933-43. [PMID: 19531563 DOI: 10.1158/1541-7786.mcr-08-0365] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Recent reports indicate that the activating transcription factor 5 (ATF5) is required for the survival of cancer cells but not for noncancer cells. However, the mechanisms by which ATF5 regulates genes and promotes cell survival are not clear. Using a cyclic amplification and selection of targets (CASTing) approach, we identified a novel ATF5 consensus DNA binding sequence. We show in C6 glioma and MCF-7 breast cancer cells that ATF5 occupies this sequence and that ATF5 activates reporter gene expression driven by this site. Conversely, reporter activity is diminished when ATF5 activity is blocked or when ATF5 expression is down-regulated by serum withdrawal. We further show that early growth response factor 1 (Egr-1), whose promoter contains two adjacent ATF5 consensus binding sites at a conserved promoter position in rat, mouse, and human, is targeted and regulated by ATF5 in C6 and MCF-7 cells. These data provide new insight on the mechanisms by which ATF5 promotes gene regulation and cancer-specific cell survival.
Collapse
Affiliation(s)
- Guangfu Li
- Department of Neural and Behavioral Sciences, Penn State University College of Medicine, Hershey, 17033, USA
| | | | | | | | | |
Collapse
|
19
|
Tao RH, Maruyama IN. All EGF(ErbB) receptors have preformed homo- and heterodimeric structures in living cells. J Cell Sci 2008; 121:3207-17. [DOI: 10.1242/jcs.033399] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) family of receptor tyrosine kinases, also known as ErbB or HER, plays crucial roles in the development of multicellular organisms. Mutations and over-expression of the ErbB receptors have been implicated in a variety of human cancers. It is widely thought that the ErbB receptors are located in the plasma membrane, and that ligand binding to the monomeric form of the receptors induces its dimeric form for activation. However, it still remains controversial whether prior to ligand binding the receptors exist as monomers or dimers on the cell surface. Using bimolecular fluorescence complementation (BiFC) assays in the present study, we demonstrate that in the absence of bound ligand, all the ErbB family members have preformed, yet inactive, homo- and heterodimers on the cell surface, except for ErbB3 homodimers and heterodimers with cleavable ErbB4, which exist primarily in the nucleus. BiFC assays of the dimerization have also suggested that the ligand-independent dimerization of the ErbB receptors occurs in the endoplasmic reticulum (ER) before newly synthesized receptor molecules reach the cell surface. Based on BiFC and mammalian two-hybrid assays, it is apparent that the intracellular domains of the receptors are responsible for the spontaneous dimer formation. These provide new insights into an understanding of transmembrane signal transduction mediated by the ErbB family members, and are relevant to the development of anti-cancer drugs.
Collapse
Affiliation(s)
- Rong-Hua Tao
- Information Processing Biology Unit, Okinawa Institute of Science and Technology, 12-2 Suzaki, Uruma, Okinawa 904-2234, Japan
| | - Ichi N. Maruyama
- Information Processing Biology Unit, Okinawa Institute of Science and Technology, 12-2 Suzaki, Uruma, Okinawa 904-2234, Japan
| |
Collapse
|
20
|
Kerppola TK. Bimolecular fluorescence complementation (BiFC) analysis as a probe of protein interactions in living cells. Annu Rev Biophys 2008; 37:465-87. [PMID: 18573091 DOI: 10.1146/annurev.biophys.37.032807.125842] [Citation(s) in RCA: 490] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein interactions are a fundamental mechanism for the generation of biological regulatory specificity. The study of protein interactions in living cells is of particular significance because the interactions that occur in a particular cell depend on the full complement of proteins present in the cell and the external stimuli that influence the cell. Bimolecular fluorescence complementation (BiFC) analysis enables direct visualization of protein interactions in living cells. The BiFC assay is based on the association between two nonfluorescent fragments of a fluorescent protein when they are brought in proximity to each other by an interaction between proteins fused to the fragments. Numerous protein interactions have been visualized using the BiFC assay in many different cell types and organisms. The BiFC assay is technically straightforward and can be performed using standard molecular biology and cell culture reagents and a regular fluorescence microscope or flow cytometer.
Collapse
Affiliation(s)
- Tom K Kerppola
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0650, USA.
| |
Collapse
|
21
|
Hu CD, Grinberg AV, Kerppola TK. Visualization of protein interactions in living cells using bimolecular fluorescence complementation (BiFC) analysis. ACTA ACUST UNITED AC 2008; Chapter 21:Unit 21.3. [PMID: 18228482 DOI: 10.1002/0471143030.cb2103s29] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein interactions integrate stimuli from different signaling pathways and developmental programs. Bimolecular fluorescence complementation (BiFC) analysis has been developed for visualization of protein interactions in living cells. This approach is based on complementation between two fragments of a fluorescent protein when they are brought together by an interaction between proteins fused to the fragments, and it enables visualization of the subcellular locations of protein interactions in the normal cellular environment. It can be used for the analysis of many protein interactions and does not require information about the structures of the interaction partners. A multicolor BiFC approach has been developed for simultaneous visualization of interactions with multiple alternative partners in the same cell, based on complementation between fragments of engineered fluorescent proteins that produce bimolecular fluorescent complexes with distinct spectral characteristics. This enables comparison of subcellular distributions of different protein complexes in the same cell and allows analysis of competition between mutually exclusive interaction partners.
Collapse
Affiliation(s)
- Chang-Deng Hu
- Howard Hughes Medical Institute and University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | | |
Collapse
|
22
|
Abstract
Autophagy is a ubiquitous degradative pathway for the bulk degradation of eukaryotic macromolecules and organelles in eukaryotic cells (Klionsky, 2005; Levine and Klionsky, 2004). Previously, the role of autophagy in turgor generation in plant pathogenic fungi was unknown. Currently, autophagy is confirmed as an important pathway for turgor accumulation in the appressorium (the tips of the invasive hyphae; Liu et al., 2007b) using a technique of targeted gene replacement, deleting the genes that code for Magnaporthe oryzae homologs of yeast autophagy-related (ATG) genes ATG2, ATG4, ATG5, ATG8, ATG9, and ATG18 (Liu et al., 2007a). All of these null mutants fail to breach the cuticle of the host. This chapter will first look at some methodologies to analyze the functions of autophagy-related gene products at the biological, cellular, and molecular level in this model plant pathogenic fungi, and then provide some research evidence of the role of autophagy in the promotion of the formation of the infection structure and pathogenicity to point out some significant areas for further research in this field.
Collapse
Affiliation(s)
- Xiao-Hong Liu
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Huajiachi Campus, Hangzhou, Zhejiang, China
| | | | | |
Collapse
|
23
|
Kerppola TK. Bimolecular fluorescence complementation: visualization of molecular interactions in living cells. Methods Cell Biol 2008; 85:431-70. [PMID: 18155474 DOI: 10.1016/s0091-679x(08)85019-4] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A variety of experimental methods have been developed for the analysis of protein interactions. The majority of these methods either require disruption of the cells to detect molecular interactions or rely on indirect detection of the protein interaction. The bimolecular fluorescence complementation (BiFC) assay provides a direct approach for the visualization of molecular interactions in living cells and organisms. The BiFC approach is based on the facilitated association between two fragments of a fluorescent protein when the fragments are brought together by an interaction between proteins fused to the fragments. The BiFC approach has been used for visualization of interactions among a variety of structurally diverse interaction partners in many different cell types. It enables detection of transient complexes as well as complexes formed by a subpopulation of the interaction partners. It is essential to include negative controls in each experiment in which the interface between the interaction partners has been mutated or deleted. The BiFC assay has been adapted for simultaneous visualization of multiple protein complexes in the same cell and the competition for shared interaction partners. A ubiquitin-mediated fluorescence complementation assay has also been developed for visualization of the covalent modification of proteins by ubiquitin family peptides. These fluorescence complementation assays have a great potential to illuminate a variety of biological interactions in the future.
Collapse
Affiliation(s)
- Tom K Kerppola
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| |
Collapse
|
24
|
Kerppola TK. Design and implementation of bimolecular fluorescence complementation (BiFC) assays for the visualization of protein interactions in living cells. Nat Protoc 2007; 1:1278-86. [PMID: 17406412 PMCID: PMC2518326 DOI: 10.1038/nprot.2006.201] [Citation(s) in RCA: 391] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Bimolecular fluorescence complementation (BiFC) analysis enables direct visualization of protein interactions in living cells. The BiFC assay is based on the discoveries that two non-fluorescent fragments of a fluorescent protein can form a fluorescent complex and that the association of the fragments can be facilitated when they are fused to two proteins that interact with each other. BiFC must be confirmed by parallel analysis of proteins in which the interaction interface has been mutated. It is not necessary for the interaction partners to juxtapose the fragments within a specific distance of each other because they can associate when they are tethered to a complex with flexible linkers. It is also not necessary for the interaction partners to form a complex with a long half-life or a high occupancy since the fragments can associate in a transient complex and un-associated fusion proteins do not interfere with detection of the complex. Many interactions can be visualized when the fusion proteins are expressed at levels comparable to their endogenous counterparts. The BiFC assay has been used for the visualization of interactions between many types of proteins in different subcellular locations and in different cell types and organisms. It is technically straightforward and can be performed using a regular fluorescence microscope and standard molecular biology and cell culture reagents.
Collapse
Affiliation(s)
- Tom K Kerppola
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.
| |
Collapse
|
25
|
Ward NE, Pellis NR, Risin SA, Risin D. Gene expression alterations in activated human T-cells induced by modeled microgravity. J Cell Biochem 2006; 99:1187-202. [PMID: 16795038 DOI: 10.1002/jcb.20988] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Studies conducted in real Space and in ground-based microgravity analog systems (MAS) have demonstrated changes in numerous lymphocyte functions. In this investigation we explored whether the observed functional changes in lymphocytes in MAS are associated with changes in gene expression. NASA-developed Rotating Wall Vessel (RWV) bioreactor was utilized as a MAS. Activated T lymphocytes were obtained by adding 100 ng/ml of anti-CD3 and 100 U/ml of IL-2 in RPMI medium to blood donor mononuclear cells for 4 days. After that the cells were washed and additionally cultured for up to 2 weeks with media (RPMI, 10% FBS and 100 U/ml IL-2) replacement every 3-4 days. Flow cytometry analysis had proven that activated T lymphocytes were the only cells remaining in culture by that time. They were split into two portions, cultured for additional 24 h in either static or simulated microgravity conditions, and used for RNA extraction. The gene expression was assessed by Affymetrix GeneChip Human U133A array allowing screening for expression of 18,400 genes. About 4-8% of tested genes responded to MG by more than a 1.5-fold change in expression; however, reproducible changes were observed only in 89 genes. Ten of these genes were upregulated and 79 were downregulated. These genes were categorized by associated pathways and viewed graphically through histogram analysis. Separate histograms of each pathway were then constructed representing individual gene expression fold changes. Possible functional consequences of the identified reproducible gene expression changes are discussed.
Collapse
|
26
|
Abstract
The visualization of protein complexes in living cells enables the examination of protein interactions in their normal environment and the determination of their subcellular localization. The bimolecular fluorescence complementation assay has been used to visualize interactions among multiple proteins in many cell types and organisms. Modified forms of this assay have been used to visualize the competition between alternative interaction partners and the covalent modification of proteins by ubiquitin-family peptides.
Collapse
Affiliation(s)
- Tom K Kerppola
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0650, USA.
| |
Collapse
|
27
|
Deppmann CD, Alvania RS, Taparowsky EJ. Cross-species annotation of basic leucine zipper factor interactions: Insight into the evolution of closed interaction networks. Mol Biol Evol 2006; 23:1480-92. [PMID: 16731568 DOI: 10.1093/molbev/msl022] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Dimeric basic leucine zipper (bZIP) factors constitute one of the most important classes of enhancer-type transcription factors. In vertebrates, bZIP factors are involved in many cellular processes, including cell survival, learning and memory, cancer progression, lipid metabolism, and a variety of developmental processes. These factors have the ability to homodimerize and heterodimerize in a specific and predictable manner, resulting in hundreds of dimers with unique effects on transcription. In recent years, several studies have described dimerization preferences for bZIP factors from different species, including Homo sapiens, Drosophila melanogaster, Arabidopsis thaliana, and Saccharomyces cerevisiae. Here, these findings are summarized as novel, graphical representations of closed, interacting protein networks. These representations combine phylogenetic information, DNA-binding properties, and dimerization preference. Beyond summarizing bZIP dimerization preferences within selected species, we have included annotation for a solitary bZIP factor found in the primitive eukaryote, Giardia lamblia, a possible evolutionary precursor to the complex networks of bZIP factors encoded by other genomes. Finally, we discuss the fundamental similarities and differences between dimerization networks within the context of bZIP factor evolution.
Collapse
|
28
|
Amoutzias GD, Bornberg-Bauer E, Oliver SG, Robertson DL. Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network. BMC Genomics 2006; 7:107. [PMID: 16674813 PMCID: PMC1479340 DOI: 10.1186/1471-2164-7-107] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Accepted: 05/04/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND bZIPs are transcription factors that are found throughout the eukarya from fungi to flowering plants and mammals. They contain highly conserved basic region (BR) and leucine zipper (LZ) domains and often function as environmental sensors. Specifically, bZIPs frequently have a role in mediating the response to oxidative stress, a crucial environmental signal that needs to be transduced to the gene regulatory network. RESULTS Based on sequence comparisons and experimental data on a number of important bZIP transcription factors, we predict which bZIPs are under redox control and which are regulated via protein phosphorylation. By integrating genomic, phylogenetic and functional data from the literature, we then propose a link between oxidative stress and the choice of interaction partners for the bZIP proteins. CONCLUSION This integration permits the bZIP dimerization network to be interpreted in functional terms, especially in the context of the role of bZIP proteins in the response to environmental stress. This analysis demonstrates the importance of abiotic factors in shaping regulatory networks.
Collapse
Affiliation(s)
- Gregory D Amoutzias
- Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Erich Bornberg-Bauer
- Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
- Bioinformatics Division, Institute of Botany, School of Biological Sciences, University of Münster, Schlossplatz 4, D4814P, Germany
| | - Stephen G Oliver
- Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - David L Robertson
- Centre for the Analysis of Biological Complexity, Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| |
Collapse
|
29
|
Thornton TM, Zullo AJ, Williams KL, Taparowsky EJ. Direct manipulation of activator protein-1 controls thymocyte proliferation in vitro. Eur J Immunol 2006; 36:160-9. [PMID: 16380965 DOI: 10.1002/eji.200535215] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
B cell activating transcription factor (BATF) belongs to the activator protein-1 (AP-1) superfamily of basic leucine zipper transcription factors and forms heterodimers with Jun that possess minimal transcriptional activity. Mice carrying a p56(lck)HA-BATF transgene were created to observe the effects of constitutive expression of this well-characterized AP-1 inhibitor on T cell proliferation. Consistent with the role of AP-1 in promoting the proliferation of many cell types, BATF-transgenic thymocytes proliferate poorly in vitro when stimulated with anti-CD3epsilon and anti-CD28 antibodies or with Concanavalin A. However, when BATF-transgenic thymocytes were stimulated using a standard treatment of PMA and ionomycin, proliferation is normal. The responsiveness to PMA and ionomycin can be attributed to the dramatic disappearance of the hemagglutinin antigen (HA)-tagged BATF protein which is a PKC-dependent process caused by the down-regulation of the p56(lck) proximal promoter coupled with the rapid turnover of the HA-BATF protein. These studies describe conditions of T cell stimulation that negatively influence transcription of the widely used p56(lck) proximal promoter expression cassette. In addition, the unique circumstances of this regulation were exploited to demonstrate that inhibition of AP-1 activity by BATF exerts a direct, and reversible, effect on T cell proliferation in vitro.
Collapse
Affiliation(s)
- Tina M Thornton
- Department of Biological Sciences and Purdue Cancer Center, Purdue University, West Lafayette, IN 479071-2054, USA
| | | | | | | |
Collapse
|
30
|
Hu CD, Grinberg AV, Kerppola TK. Visualization of protein interactions in living cells using bimolecular fluorescence complementation (BiFC) analysis. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2005; Chapter 19:19.10.1-19.10.21. [PMID: 18429278 DOI: 10.1002/0471140864.ps1910s41] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein interactions integrate stimuli from different signaling pathways and developmental programs. Bimolecular fluorescence complementation (BiFC) analysis has been developed for visualization of protein interactions in living cells. This approach is based on complementation between two fragments of a fluorescent protein when they are brought together by an interaction between proteins fused to the fragments, and it enables visualization of the subcellular locations of protein interactions in the normal cellular environment. It can be used for the analysis of many protein interactions and does not require information about the structures of the interaction partners. A multicolor BiFC approach has been developed for simultaneous visualization of interactions with multiple alternative partners in the same cell, based on complementation between fragments of engineered fluorescent proteins that produce bimolecular fluorescent complexes with distinct spectral characteristics. This enables comparison of subcellular distributions of different protein complexes in the same cell and allows analysis of competition between mutually exclusive interaction partners.
Collapse
Affiliation(s)
- Chang-Deng Hu
- Howard Hughes Medical Institute and University of Michigan Medical School, Ann Arbor, Michigan
| | - Asya V Grinberg
- Howard Hughes Medical Institute and University of Michigan Medical School, Ann Arbor, Michigan
| | - Tom K Kerppola
- Howard Hughes Medical Institute and University of Michigan Medical School, Ann Arbor, Michigan
| |
Collapse
|
31
|
Blanco FA, Judelson HS. A bZIP transcription factor from Phytophthora interacts with a protein kinase and is required for zoospore motility and plant infection. Mol Microbiol 2005; 56:638-48. [PMID: 15819621 DOI: 10.1111/j.1365-2958.2005.04575.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Zoospores are critical in the disease cycle of Phytophthora infestans, a member of the oomycete group of fungus-like microbes and the cause of potato late blight. A protein kinase induced during zoosporogenesis, Pipkz1, was shown to interact in the yeast two-hybrid system with a putative bZIP transcription factor. This interaction was confirmed in vitro using a pull-down assay. The transcription factor gene, Pibzp1, was single copy and expressed in all tissues. Transformants of P. infestans stably silenced for Pibzp1 were generated using plasmids expressing its coding region in sense or antisense orientations. A protoplast transformation method induced silencing more efficiently than transformation by an electroporation scheme. Wild-type and silenced strains exhibited no differences in hyphal growth or morphology, mating, sporangia production or zoospore release. However, zoospores from the mutants spun in tight circles, instead of exhibiting the normal pattern of straight swimming punctuated by turns. Zoospore encystment was unaffected by silencing, but cysts germinated more efficiently than controls. Germinated cysts from the mutants failed to develop appressoria and were unable to infect plants; however, they could colonize wounded tissue. These phenotypes indicate that Pibzp1 is a key regulator of several stages of the zoospore-mediated infection pathway.
Collapse
Affiliation(s)
- Flavio A Blanco
- Center for Plant Cell Biology and Department of Plant Pathology, University of California, Riverside, CA 92521, USA
| | | |
Collapse
|
32
|
Parker GE, West BE, Witzmann FA, Rhodes SJ. Serine/threonine/tyrosine phosphorylation of the LHX3 LIM-homeodomain transcription factor. J Cell Biochem 2005; 94:67-80. [PMID: 15517599 DOI: 10.1002/jcb.20287] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
LHX3 is a LIM homeodomain transcription factor with essential roles in pituitary and motor neuron development in mammals. Patients with mutations in the LHX3 gene have combined pituitary hormone deficiency and other symptoms. In this study, we show that the LHX3 protein can be modified post-translationally by phosphorylation. LHX3 can serve as a substrate for protein kinase C and casein kinase II. Overexpression of these kinases reduces the transcriptional capacity of LHX3 to activate target genes. Following exposure of LHX3 to cellular kinases, mass spectrometry was used to map the phosphorylation of five amino acid residues within the human LHX3a isoform. Two phosphorylated residues (threonine 63 and serine 71) lie within the first LIM domain of the protein. Three other modified amino acids (tyrosine 227, serine 234, and serine 238) are located in the carboxyl terminus. Targeted replacement of these amino acids with non-modifiable residues significantly reduced the ability of LHX3 to activate both synthetic and pituitary hormone reporter genes. However, the amino acid replacements did not significantly affect the capability of LHX3 to interact with the NLI, PIT1, and MRG1 partner proteins, or its ability to bind to a high affinity DNA site. In conclusion, we have identified unique amino acids within LHX3 that are important for its transcriptional activity and are phosphorylated.
Collapse
Affiliation(s)
- Gretchen E Parker
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202-5132, USA
| | | | | | | |
Collapse
|
33
|
Hu C, Grinberg AV, Kerppola TK. Visualization of Protein Interactions in Living Cells Using Bimolecular Fluorescence Complementation (
Bi
FC
) Analysis. ACTA ACUST UNITED AC 2005. [DOI: 10.1002/0471143030.cb2103s26] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chang‐Deng Hu
- Howard Hughes Medical Institute and University of Michigan Medical School Ann Arbor Michigan
| | - Asya V. Grinberg
- Howard Hughes Medical Institute and University of Michigan Medical School Ann Arbor Michigan
| | - Tom K. Kerppola
- Howard Hughes Medical Institute and University of Michigan Medical School Ann Arbor Michigan
| |
Collapse
|